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2021-02-01gnu: avogadro: Wrap with GUIX_PYTHONPATH....* gnu/packages/chemistry.scm (avogadro) [phases]: Delete trailing #t. {wrap-program}: Replace PYTHONPATH with GUIX_PYTHONPATH. Maxim Cournoyer
2021-02-01gnu: Adjust package collection to Wrap using GUIX_PYTHONPATH....This change was automated using: $ git ls-files | grep .scm | \ xargs sed 's/(getenv "PYTHONPATH")/(getenv "GUIX_PYTHONPATH")/' -i $ git ls-files | grep .scm | \ xargs sed 's/`("PYTHONPATH"/`("GUIX_PYTHONPATH"/' -i * gnu/packages/admin.scm (nmap): (dstat): Wrap using GUIX_PYTHONPATH. * gnu/packages/audio.scm (jack-2): (carla): Likewise. * gnu/packages/benchmark.scm (fio): Likewise. * gnu/packages/bioinformatics.scm (couger): Likewise. (gess, find-circ, filtlong, nanopolish): Likewise. * gnu/packages/cdrom.scm (cdemu-client): Likewise. * gnu/packages/chemistry.scm (avogadro): Likewise. * gnu/packages/connman.scm (econnman): Likewise. * gnu/packages/cups.scm (hplip): Likewise. * gnu/packages/debug.scm (scanmem): Likewise. * gnu/packages/display-managers.scm (lightdm): Likewise. * gnu/packages/ebook.scm (cozy): Likewise. * gnu/packages/education.scm (anki): Likewise. * gnu/packages/engineering.scm (kicad, volk, freecad): Likewise. * gnu/packages/game-development.scm (renpy): Likewise. * gnu/packages/games.scm (roguebox-adventures) (seahorse-adventures, kajongg): Likewise. * gnu/packages/gimp.scm (gimp, glimpse): Likewise. * gnu/packages/glib.scm (itstool): Likewise. * gnu/packages/gnome.scm (gnome-music, gtg, rhythmbox): Likewise. (eolie, d-feet, gedit, caribou, gnome-shell, authenticator) (gnome-todo, orca, passwordsafe, terminator, setzer) (libratbag, komikku): Likewise. * gnu/packages/gps.scm (gpsd): Likewise. * gnu/packages/gtk.scm (gtk-doc): Likewise. * gnu/packages/ibus.scm (ibus, ibus-libpinyin, ibus-anthy) (ibus-libhangul): Likewise. * gnu/packages/inkscape.scm (inkscape-1.0): Likewise. * gnu/packages/linux.scm (bcc): Likewise. * gnu/packages/mail.scm (notifymuch): Likewise. * gnu/packages/maths.scm (units): Likewise. * gnu/packages/music.scm (solfege): Likewise. * gnu/packages/networking.scm (blueman): Likewise. * gnu/packages/patchutils.scm (patchwork): Likewise. * gnu/packages/photo.scm (rapid-photo-downloader, entangle): Likewise. * gnu/packages/plotutils.scm (asymptote): Likewise. * gnu/packages/presentation.scm (presentty): Likewise. * gnu/packages/screen.scm (byobu): Likewise. * gnu/packages/storage.scm (ceph): Likewise. * gnu/packages/syndication.scm (liferea): Likewise. * gnu/packages/task-management.scm (blanket): Likewise. * gnu/packages/text-editors.scm (manuskript): Likewise. * gnu/packages/version-control.scm (gitless, cgit, git-when-merged) (git-imerge): Likewise. * gnu/packages/video.scm (pitivi): Likewise. * gnu/packages/virtualization.scm (criu): Likewise. * gnu/packages/xfce.scm (catfish): Likewise. Maxim Cournoyer
2020-07-12gnu: Remove ".git" from "https://github/…/….git"....Until now, 'lookup-origin' and thus 'lookup-origin-revision' in (guix swh) would sometimes return #f for these because the ".git" URLs are redirects to the non-".git" URLs. Consequently, 'guix lint -c archival' would keep saying "scheduled Software Heritage archival"; likewise, the fallback download code would fail. * gnu/packages/ada.scm, gnu/packages/admin.scm, gnu/packages/aidc.scm, gnu/packages/algebra.scm, gnu/packages/android.scm, gnu/packages/animation.scm, gnu/packages/arcan.scm, gnu/packages/assembly.scm, gnu/packages/audio.scm, gnu/packages/authentication.scm, gnu/packages/avr.scm, gnu/packages/axoloti.scm, gnu/packages/backup.scm, gnu/packages/bash.scm, gnu/packages/benchmark.scm, gnu/packages/bioconductor.scm, gnu/packages/bioinformatics.scm, gnu/packages/bittorrent.scm, gnu/packages/boost.scm, gnu/packages/build-tools.scm, gnu/packages/c.scm, gnu/packages/calendar.scm, gnu/packages/cdrom.scm, gnu/packages/check.scm, gnu/packages/chemistry.scm, gnu/packages/chez.scm, gnu/packages/clojure.scm, gnu/packages/code.scm, gnu/packages/compression.scm, gnu/packages/compton.scm, gnu/packages/coq.scm, gnu/packages/cpp.scm, gnu/packages/cran.scm, gnu/packages/crypto.scm, gnu/packages/curl.scm, gnu/packages/databases.scm, gnu/packages/datastructures.scm, gnu/packages/debug.scm, gnu/packages/disk.scm, gnu/packages/distributed.scm, gnu/packages/django.scm, gnu/packages/dlang.scm, gnu/packages/dns.scm, gnu/packages/docker.scm, gnu/packages/education.scm, gnu/packages/efi.scm, gnu/packages/elixir.scm, gnu/packages/emacs-xyz.scm, gnu/packages/embedded.scm, gnu/packages/emulators.scm, gnu/packages/engineering.scm, gnu/packages/erlang.scm, gnu/packages/fabric-management.scm, gnu/packages/file-systems.scm, gnu/packages/finance.scm, gnu/packages/firmware.scm, gnu/packages/flashing-tools.scm, gnu/packages/fonts.scm, gnu/packages/fontutils.scm, gnu/packages/fpga.scm, gnu/packages/game-development.scm, gnu/packages/games.scm, gnu/packages/genealogy.scm, gnu/packages/genimage.scm, gnu/packages/geo.scm, gnu/packages/gimp.scm, gnu/packages/gl.scm, gnu/packages/gnome-xyz.scm, gnu/packages/gnome.scm, gnu/packages/gnuzilla.scm, gnu/packages/golang.scm, gnu/packages/gpodder.scm, gnu/packages/graph.scm, gnu/packages/graphics.scm, gnu/packages/graphviz.scm, gnu/packages/groff.scm, gnu/packages/groovy.scm, gnu/packages/gtk.scm, gnu/packages/guile-xyz.scm, gnu/packages/guile.scm, gnu/packages/hardware.scm, gnu/packages/haskell-apps.scm, gnu/packages/haskell-xyz.scm, gnu/packages/hexedit.scm, gnu/packages/i2p.scm, gnu/packages/ibus.scm, gnu/packages/image-processing.scm, gnu/packages/image-viewers.scm, gnu/packages/image.scm, gnu/packages/ipfs.scm, gnu/packages/java-graphics.scm, gnu/packages/java-maths.scm, gnu/packages/java.scm, gnu/packages/javascript.scm, gnu/packages/jrnl.scm, gnu/packages/julia.scm, gnu/packages/jupyter.scm, gnu/packages/kodi.scm, gnu/packages/language.scm, gnu/packages/lego.scm, gnu/packages/less.scm, gnu/packages/libusb.scm, gnu/packages/linux.scm, gnu/packages/lirc.scm, gnu/packages/lisp-xyz.scm, gnu/packages/llvm.scm, gnu/packages/logging.scm, gnu/packages/lolcode.scm, gnu/packages/lua.scm, gnu/packages/lxde.scm, gnu/packages/lxqt.scm, gnu/packages/machine-learning.scm, gnu/packages/mail.scm, gnu/packages/markup.scm, gnu/packages/maths.scm, gnu/packages/maven.scm, gnu/packages/mes.scm, gnu/packages/messaging.scm, gnu/packages/monitoring.scm, gnu/packages/mpd.scm, gnu/packages/music.scm, gnu/packages/networking.scm, gnu/packages/node-xyz.scm, gnu/packages/ocaml.scm, gnu/packages/ocr.scm, gnu/packages/onc-rpc.scm, gnu/packages/opencl.scm, gnu/packages/opencog.scm, gnu/packages/pantheon.scm, gnu/packages/password-utils.scm, gnu/packages/patchutils.scm, gnu/packages/pdf.scm, gnu/packages/perl6.scm, gnu/packages/phabricator.scm, gnu/packages/popt.scm, gnu/packages/printers.scm, gnu/packages/prolog.scm, gnu/packages/protobuf.scm, gnu/packages/pulseaudio.scm, gnu/packages/python-crypto.scm, gnu/packages/python-web.scm, gnu/packages/python-xyz.scm, gnu/packages/qt.scm, gnu/packages/radio.scm, gnu/packages/rails.scm, gnu/packages/rdf.scm, gnu/packages/rednotebook.scm, gnu/packages/rpc.scm, gnu/packages/rsync.scm, gnu/packages/ruby.scm, gnu/packages/rust.scm, gnu/packages/scheme.scm, gnu/packages/screen.scm, gnu/packages/security-token.scm, gnu/packages/selinux.scm, gnu/packages/serialization.scm, gnu/packages/shells.scm, gnu/packages/shellutils.scm, gnu/packages/simh.scm, gnu/packages/sml.scm, gnu/packages/ssh.scm, gnu/packages/statistics.scm, gnu/packages/stenography.scm, gnu/packages/sync.scm, gnu/packages/syncthing.scm, gnu/packages/synergy.scm, gnu/packages/telephony.scm, gnu/packages/terminals.scm, gnu/packages/tex.scm, gnu/packages/texinfo.scm, gnu/packages/text-editors.scm, gnu/packages/textutils.scm, gnu/packages/time.scm, gnu/packages/tmux.scm, gnu/packages/tor.scm, gnu/packages/toys.scm, gnu/packages/version-control.scm, gnu/packages/video.scm, gnu/packages/vim.scm, gnu/packages/virtualization.scm, gnu/packages/vlang.scm, gnu/packages/vnc.scm, gnu/packages/vpn.scm, gnu/packages/web-browsers.scm, gnu/packages/web.scm, gnu/packages/wireservice.scm, gnu/packages/wm.scm, gnu/packages/wxwidgets.scm, gnu/packages/xdisorg.scm, gnu/packages/xml.scm, gnu/packages/xorg.scm, tests/lint.scm: Remove trailing ".git" from 'git-reference' URL. Ludovic Courtès
2020-05-04gnu: Add gromacs....* gnu/packages/chemistry.scm (gromacs): New variable. * gnu/packages/patches/gromacs-tinyxml2.patch: New file... * gnu/local.mk (dist_patch_DATA): ...add it here. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Vincent Legoll
2020-05-04gnu: Add tng....* gnu/packages/chemistry.scm (tng): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Vincent Legoll
2020-04-26gnu: nmoldyn: Adjust for Guile 3.0....* gnu/packages/chemistry.scm (nmoldyn)[arguments]: Provide explicit destination in calls to FORMAT. Marius Bakke
2020-03-05gnu: domainfinder: Update home page URI....* gnu/packages/chemistry.scm (domainfinder)[home-page]: Update URI. Björn Höfling
2020-03-05gnu: nmoldyn: Upate home page URI....* gnu/packages/chemistry.scm (nmoldyn)[home-page]: Update URI. Björn Höfling
2019-11-21gnu: nmoldyn: New source code location....* gnu/packages/chemistry.scm (nmoldyn): New source code location. Following the annoucement of Bitbucket to delete all Mercurial repositories in June 2020, the source code has been migrated to GitHub. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Konrad Hinsen
2019-02-08gnu: avogadro: Don't use unstable tarball....* gnu/packages/chemistry.scm (avogadro)[source]: Use GIT-FETCH and GIT-FILE-NAME. Tobias Geerinckx-Rice
2019-01-15gnu: Separate Python core packages from the rest....* gnu/packages/python.scm: Move hundreds of package definitions from here... * gnu/packages/python-xyz.scm: ...to this new module. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. * gnu/packages/ada.scm, gnu/packages/admin.scm, gnu/packages/android.scm, gnu/packages/audio.scm, gnu/packages/backup.scm, gnu/packages/benchmark.scm, gnu/packages/bioinformatics.scm, gnu/packages/bittorrent.scm, gnu/packages/calendar.scm, gnu/packages/check.scm, gnu/packages/chemistry.scm, gnu/packages/cluster.scm, gnu/packages/compression.scm, gnu/packages/connman.scm, gnu/packages/crypto.scm, gnu/packages/cups.scm, gnu/packages/databases.scm, gnu/packages/dav.scm, gnu/packages/direct-connect.scm, gnu/packages/disk.scm, gnu/packages/django.scm, gnu/packages/dlang.scm, gnu/packages/docker.scm, gnu/packages/ebook.scm, gnu/packages/elf.scm, gnu/packages/emacs.scm, gnu/packages/emulators.scm, gnu/packages/engineering.scm, gnu/packages/enlightenment.scm, gnu/packages/finance.scm, gnu/packages/fltk.scm, gnu/packages/fontutils.scm, gnu/packages/freedesktop.scm, gnu/packages/game-development.scm, gnu/packages/games.scm, gnu/packages/geo.scm, gnu/packages/gl.scm, gnu/packages/glib.scm, gnu/packages/gnome.scm, gnu/packages/gnupg.scm, gnu/packages/gnuzilla.scm, gnu/packages/graph.scm, gnu/packages/graphics.scm, gnu/packages/graphviz.scm, gnu/packages/gtk.scm, gnu/packages/ham-radio.scm, gnu/packages/image-processing.scm, gnu/packages/image-viewers.scm, gnu/packages/image.scm, gnu/packages/irc.scm, gnu/packages/jrnl.scm, gnu/packages/julia.scm, gnu/packages/kde-frameworks.scm, gnu/packages/key-mon.scm, gnu/packages/libffi.scm, gnu/packages/libreoffice.scm, gnu/packages/libusb.scm, gnu/packages/lirc.scm, gnu/packages/logging.scm, gnu/packages/machine-learning.scm, gnu/packages/mail.scm, gnu/packages/mate.scm, gnu/packages/maths.scm, gnu/packages/medical.scm, gnu/packages/messaging.scm, gnu/packages/monitoring.scm, gnu/packages/mp3.scm, gnu/packages/mpd.scm, gnu/packages/music.scm, gnu/packages/networking.scm, gnu/packages/nutrition.scm, gnu/packages/openldap.scm, gnu/packages/openstack.scm, gnu/packages/package-management.scm, gnu/packages/password-utils.scm, gnu/packages/patchutils.scm, gnu/packages/pdf.scm, gnu/packages/photo.scm, gnu/packages/polkit.scm, gnu/packages/protobuf.scm, gnu/packages/python-crypto.scm, gnu/packages/python-web.scm, gnu/packages/qt.scm, gnu/packages/rdf.scm, gnu/packages/ruby.scm, gnu/packages/search.scm, gnu/packages/selinux.scm, gnu/packages/serialization.scm, gnu/packages/shells.scm, gnu/packages/simulation.scm, gnu/packages/ssh.scm, gnu/packages/statistics.scm, gnu/packages/storage.scm, gnu/packages/sync.scm, gnu/packages/terminals.scm, gnu/packages/textutils.scm, gnu/packages/time.scm, gnu/packages/tls.scm, gnu/packages/tor.scm, gnu/packages/tryton.scm, gnu/packages/version-control.scm, gnu/packages/video.scm, gnu/packages/virtualization.scm, gnu/packages/vpn.scm, gnu/packages/web-browsers.scm, gnu/packages/web.scm, gnu/packages/wicd.scm, gnu/packages/xdisorg.scm, gnu/packages/xorg.scm: Update module references. Ricardo Wurmus
2018-12-17gnu: avogadro: Don't hardcode python version....* gnu/packages/chemistry.scm (avogadro)[arguments]: Replace hardcoded python version with parametrized one. Efraim Flashner
2018-08-25gnu: Add avogadro....* gnu/packages/chemistry.scm (avogadro): New variable. * gnu/packages/patches/avogadro-boost148.patch, gnu/packages/patches/avogadro-eigen3-update.patch, gnu/packages/patches/avogadro-python-eigen-lib.patch: New files. * gnu/local.mk (dist_patch_DATA): Add them. Kei Kebreau
2018-07-22gnu: chemistry.scm: Add missing import....This is a follow-up to commit eb5ece73a84439d21219a802c0dcb88d54046371. * gnu/packages/chemistry.scm: Import (gnu packages). Marius Bakke
2018-07-21gnu: openbabel: Fix crash when opening NWChem output files....* gnu/packages/patches/openbabel-fix-crash-on-nwchem-output.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/chemistry.scm (openbabel)[source]: Use it. Kei Kebreau
2018-07-17gnu: Add openbabel....* gnu/packages/chemistry.scm (openbabel): New variable. Kei Kebreau
2018-07-13gnu: Add inchi....* gnu/packages/chemistry.scm (inchi): New variable. Kei Kebreau
2018-03-17gnu: Fix common unquote typos....It's easy to mistype ‘("foo" foo)’ as ‘("foo", foo)’ (which also works). Fix such typos for the proper edification of our young. * gnu/packages/android.scm: Move unquotes to their operands. * gnu/packages/bootloaders.scm: Likewise. * gnu/packages/build-tools.scm: Likewise. * gnu/packages/chemistry.scm: Likewise. * gnu/packages/compression.scm: Likewise. * gnu/packages/connman.scm: Likewise. * gnu/packages/django.scm: Likewise. * gnu/packages/emulators.scm: Likewise. * gnu/packages/engineering.scm: Likewise. * gnu/packages/file-systems.scm: Likewise. * gnu/packages/freedesktop.scm: Likewise. * gnu/packages/games.scm: Likewise. * gnu/packages/gimp.scm: Likewise. * gnu/packages/gl.scm: Likewise. * gnu/packages/gnome.scm: Likewise. * gnu/packages/graphics.scm: Likewise. * gnu/packages/haskell.scm: Likewise. * gnu/packages/irc.scm: Likewise. * gnu/packages/julia.scm: Likewise. * gnu/packages/kde-frameworks.scm: Likewise. * gnu/packages/linux.scm: Likewise. * gnu/packages/lua.scm: Likewise. * gnu/packages/mail.scm: Likewise. * gnu/packages/make-bootstrap.scm: Likewise. * gnu/packages/messaging.scm: Likewise. * gnu/packages/music.scm: Likewise. * gnu/packages/networking.scm: Likewise. * gnu/packages/ocaml.scm: Likewise. * gnu/packages/perl.scm: Likewise. * gnu/packages/python.scm: Likewise. * gnu/packages/python-web.scm: Likewise. * gnu/packages/qt.scm: Likewise. * gnu/packages/ratpoison.scm: Likewise. * gnu/packages/sdl.scm: Likewise. * gnu/packages/sml.scm: Likewise. * gnu/packages/terminals.scm: Likewise. * gnu/packages/text-editors.scm: Likewise. * gnu/packages/video.scm: Likewise. * gnu/packages/virtualization.scm: Likewise. * gnu/packages/vulkan.scm: Likewise. * gnu/packages/wget.scm: Likewise. * gnu/packages/wine.scm: Likewise. * gnu/packages/wm.scm: Likewise. * gnu/packages/xdisorg.scm: Likewise. * gnu/packages/xml.scm: Likewise. * gnu/packages/xorg.scm: Likewise. Tobias Geerinckx-Rice
2018-01-05gnu: Add nmoldyn....* gnu/packages/chemistry.scm (nmoldyn): New variable. Signed-off-by: Leo Famulari <leo@famulari.name> Konrad Hinsen
2018-01-05gnu: Add domainfinder....* gnu/packages/chemistry.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. Signed-off-by: Leo Famulari <leo@famulari.name> Konrad Hinsen